Chapter 5:�Global biogeochemical cycles

• The elemental composition of the Earth has remained essentially unchanged over its 4.5 Gyr history
• Extraterrestrial inputs (e.g., from meteorites, cometary material) have been relatively unimportant
• Escape to space has been restricted by gravity

​

• Most abundant elements, in order: oxygen (in solid earth!), iron (core), silicon (mantle), hydrogen (oceans), nitrogen, carbon, sulfur.

Brief history of Earth’s atmosphere

Outgassing

N₂

​

CO₂

​

H₂O

​

​

oceans form

CO₂

dissolves

Life forms in oceans

Onset of

photosynthesis

​

O₂

O₂ reaches current levels; life invades continents

4.5 Gy

B.P

4 Gy

B.P.

3.5 Gy

B.P.

0.4 Gy

B.P.

present

Evolution of oxygen and ozone over Earth’s history

RUNAWAY GREENHOUSE EFFECT ON VENUS

EARTH

VENUS

due to accumulation of water vapor from volcanic outgassing early in its history

…did not happen on Earth because farther from Sun; as water accumulated it reached saturation and precipitated, forming the oceans

Comparing the atmospheres of Earth and Venus

Biogeochemical cycling of elements:�examples of major processes

Physical exchange, redox chemistry, biochemistry are involved

Elementary vs. stoichiometric reactions

An elementary reaction is due to actual collision of reactants, from which the kinetics can be deduced:

A

B

AB*

C

D

A + B → C + D

A stoichiometric reaction is one that describes the net outcome of a reaction sequence, without any information on kinetics or mechanism. For example, combustion of a hydrocarbon C_xH_y is described stoichiometrically by

​

​

This can provide useful accounting information but no kinetic information

Redox reactions

oxidant + reductant → products

I want electrons! I want to get rid of electrons!

Let’s do it!

An atom minimizes energy by filling lowest-energy orbitals in its outermost (valence) electron shell: this is done by acquiring or donating electrons through bonding

First valence shell has 2 electrons, second has 8; third has 8, ..

Some handy rules for figuring out the oxidation state of an element in a molecule:

• A neutral molecule has total oxidation state 0
• Bound oxygen has oxidation state -II
• Bound hydrogen has oxidation state +I

reductant gets oxidized:

its oxidation state increases

Electronic configuration

1s²2s²2p⁶3s²3p⁶

1^st valence shell: 1s² (2 electrons)

2^nd valence shell: 2s²2p⁶ (8 electrons)

3^rd valence shell: 3s²3p⁶ (8 electrons)

In periodic table, atomic number gives number of electrons in neutral/unbound atom:

this corresponds to oxidation state zero (0) for that element. Oxidation state increases if atom acquires electrons, decreases if it donates.

oxidant gets reduced:

its oxidation state decreases

Periodic table of elements showing atomic numbers

Oxidation states of nitrogen

N has 7 electrons 1s²2s²2p³, so 5 in valence shell� 🢧9 oxidation states from –3 to +5

Oxidation of atmospheric N₂

Consider air brought to very high temperature in combustion chamber or lightning bolt; this enables the thermal decomposition of atmospheric O₂ (thermolysis):

Where ‘M’ is any molecule that collides with O₂, converting kinetic to chemical energy; if chemical energy is larger than O₂ bond strength then the O₂ molecule decomposes.

A catalytic mechanism follows oxidizing N₂ to NO (Zeldovich mechanism):

NO is then oxidized to HNO₃ in the atmosphere:

HNO₃ is the most oxidized form of N and is eventually removed from atmosphere by deposition

Reduction of atmospheric N₂

N₂ + 3H₂

2NH₃

high T, p

metal catalyst

enabled 20^th century population growth through fertilizer production

Fritz Haber

Carl Bosch

Nitrogen-fixing bacteria:

N₂

NH₃

organic N

Industrial production of NH₃ fertilizer (Haber-Bosch process):

The nitrogen cycle: major processes

Nitrogen fixation refers to conversion of N₂ to biologically usable forms

(oxic)

(anoxic)

Box model of the nitrogen cycle

Some lifetimes:

Inadvertent fertilization of the biosphere

fertilizer

NH₃

NO

HNO₃

atmosheric transport

NH₃ and HNO₃

deposition

Annual N deposition (GEOS-Chem model)

• N deposition exceeding critical load damages native ecosystems
• But it increases carbon storage…

Zhang et al. [2012]

critical load

natural anthropogenic

Nitrous oxide (N₂O): low-yield product �of biological nitrification and denitrification

Important as

• source of NO_x radicals in stratosphere
• greenhouse gas

IPCC [2022]

Increase is driven by agriculture

Fast oxygen cycle: atmosphere biosphere

• Source of O₂: photosynthesis

nCO₂ + nH₂O → (CH₂O)_n + nO₂

​

• Sink: respiration/decay

(CH₂O)_n + nO₂ → nCO₂ + nH₂O

O₂

CO₂

orgC

orgC

litter

Net photosynthesis

by green plants:

320 Pg O a^-1

decay

O₂ lifetime: 3800 years

1.2×10⁶ Pg O

biological material

(orgC)

320 Pg O a^-1

…but abundance of organic carbon in biosphere/soil/ocean reservoirs is too small to control atmospheric O₂ levels

If photosynthesis stopped, only 3300 Pg C would get oxidized and this would consume (3300/12)x32 = 8800 Pg O or less than 1% of O₂ reservoir

Slow oxygen cycle: atmosphere-lithosphere

orgC: 1x10⁷ Pg C

O₂: 1.2x10⁶ Pg O

O₂ lifetime: 3 million years

regulates concentrations of atmospheric O₂

FeS₂: 5x10⁶ Pg S

Increase in atmospheric CO₂ from fossil fuel combustion

https://www.esrl.noaa.gov/gmd/ccgg/trends

Ice core records for past 2,000 years

emission: 10 billion tons of carbon

per year (2023)

January 2025: 427 ppm

Growth rate: 3 ppm/year = 5 billion tons C /year

Trends in fossil fuel CO₂ emissions

https://ourworldindata.org/co2-emissions

2023: 10.1 billion tons C

US: 3.9 tons C per capita per year

1^st IPCC report

Kyoto protocol

Paris agreement

Annual National CO₂ Emissions (1960-2024)

�The 2024 projections are based on preliminary data and modelling. �‘Bunkers’ are fossil fuels (oil) used for shipping and aviation in international territory�Source: Friedlingstein et al 2024; Global Carbon Project 2024

Annual per capita CO₂ emissions (1960- 2022)

Countries have a broad range of per capita emissions reflecting their national circumstances

International aviation and maritime shipping (bunker fuels) contributed 2.8% of global emissions in 2022.

Source: Friedlingstein et al 2023; Global Carbon Project 2023

�

Need to understand the carbon sinks

Only about half of emitted CO₂ remains in atmosphere

Pg C yr^-1

This airborne fraction (AF) of CO₂ has remained remarkably constant at 44% over past 60 years

IPCC AR6 [2022]

The natural carbon cycle: major processes

Uptake of CO₂ by the oceans

Dominant species at ocean pH (8.2) is HCO₃^-

Equilibrium partitioning of CO₂�between atmosphere and global ocean

At pH 8.2, only 1.6% of total carbon is in the atmosphere

​

Air (N_a moles, pressure p):

N_CO2(g) moles of CO₂

Ocean (volume V_o):

N_CO2(aq) moles of dissolved CO₂

Fraction F of total CO₂ in atmosphere:

Replace:

The natural (preindustrial) carbon cycle: masses and flows

NPP is net primary production = photosynthesis – respiration by green plants

100 m deep

Perturbing the carbon cycle

As we add CO₂ to the atmosphere, how will the sinks respond?

• If ocean response was linear (first-order), then the added CO₂ would go away (in the deep ocean) on a time scale of ~20 years

But CO₂(g) ↗ 🢡 [H⁺] ↗ 🢡 F ↗ 🢡 positive feedback to perturbation

• If land response is linear (first-order), then the added CO₂ would largely go away (in the soil) on a time scale of ~100 years

But photosynthesis is limited by factors other than CO₂ availability (hv, water, nutrients, land management).

Alkalinity controls the uptake of CO₂ by ocean

[Na⁺] +2[Mg²⁺] + 2[Ca²⁺] + [K⁺] + [H+] = [Cl^-] + 2[SO₄^2-] + [HCO₃^-] +2[CO₃^2-] + [OH^-]

Electroneutrality equation:

Mean ionic composition of seawater:

ions originate from dissolution of rocks on geologic time scales

The only ions that can take up added acid are HCO₃^- and CO₃^2-;

this capacity is called the alkalinity of the system

[Alk] = [HCO₃^-] +2[CO₃^2-] = [Na⁺] +2[Mg²⁺] + 2[Ca²⁺] + [K⁺] – [Cl^-] - 2[SO₄^2-] = 2.3x10^-3 M

[H⁺] and [OH^-] are small compared to other terms

CO₂ uptake by the ocean conserves alkalinity

• How to do this while increasing ocean carbon: convert CO₃^2- to HCO₃^-

As p_CO2 increases, [CO₃^2-] decreases and the ability of the ocean to take up CO₂ decreases

• Increasing Alk to take up more CO₂ requires dissolution of sediments:

which takes thousands of years

[Alk] = [HCO₃^-] +2[CO₃^2-] = [Na⁺] +2[Mg²⁺] + 2[Ca²⁺] + [K⁺] – [Cl^-] - 2[SO₄^2-] = 2.3x10^-3 M

this does not change

Efficiency of the ocean as a sink for added CO₂

How does a CO₂ addition dN_CO2 partition between atmosphere and ocean at equilibrium?

🢡 19% of added CO₂ remains in atmosphere at equilibrium, vs. 1.6% in linear system

🢡

This assumes equilibrium with whole ocean (mixing timescale of 200 years)

For equilibrium with surface ocean(3% of total ocean) we find f = 0.88: 88% remains! Ocean sink is therefore strongly controlled by circulation.

Global circulation of the ocean

thermocline

(inversion)

Global ocean conveyor belt

Red: surface flow

blue: deep flow

Models and observations of ocean sink for added CO₂

23% (best estimate)

f = 0.77

IPCC AR6 [2022]

Acidification of the ocean from increasing CO₂

CO₂

H₂CO₃

HCO₃^_ + H⁺

Air

​

Ocean

Acidification of the ocean endangers marine biosphere by making it more difficult to form calcium carbonate shells

Change in ocean pH since preindustrial

WMO (2022), GLODAP

0.1 pH decrease

means 26% acidity increase

Evidence of C uptake by northern mid-latitudes biosphere: �N–S hemisphere difference

Science, 247, 1431-1438 (1990)

Observations

(1981-1987)

Model (no net

biospheric uptake)

Tans

Fung

Takahashi

Carbon sink from reforestation:�Harvard Forest in Petersham, central Mass. – late 1800s and now

Global net biome production (NB) is tiny fraction of photosynthesis�- and can easily change sign in response to external factors

Current estimate of global land sink:

Monitoring of land sink with observations of atmospheric O₂

• Combustion:

consume (1+y/4x) O₂ per CO₂ produced

• Photosynthesis: produce 1 O₂ per CO₂ consumed

​

• Ocean uptake: O₂-neutral

IPCC AR5 [2014]

CO₂

O₂

Land sink can also be estimated as a residual

Source: CDIAC; NOAA-ESRL; Houghton and Nassikas 2017; Hansis et al 2015; Joos et al 2013;�

https://ocov2.jpl.nasa.gov

Future projections of CO₂ emission (IPCC AR6, 2022)

+4.4^oC relative to 1850-1900

+2.4^oC

+1.6^oC

IPCC AR6 [2022]

Fate of emitted CO₂ for the different scenarios

Acceleration in growth of CO₂, CH₄ and N₂O

Carbon dioxide (CO₂, ppm)

Methane (CH₄, ppb)

Nitrous oxide (N₂O, ppb)

WMO GHG Bulletin, 2025

• Acceleration in the growth of all three greenhouse gases over past two decades
• In 2024, carbon dioxide concentrations rose 3.7 ppm due to weakening sinks
• Methane and nitrous oxide growth declined somewhat (El Niño related)

Tracking progress toward climate mitigation

GCB 2025, Glenn Peters

• Fossil emissions are growing more slowly (in contrast to concentrations)
• Fossil CO₂ & CH₄ track middle of range SSPs, e.g., SSP4-6.0 and SSP2-4.5